This document walks through the Reorienting to Recovery’s Recovery Definition and evaluates how the Kitchen Sink Blended Scenario Performs. It provides summary statistics and visualizations to evaluate recovery according to defined thresholds recovery metrics (Threshold Recovery Metrics table below) and to explore results associated with non thereshold biological metrics (Additional Biological Metrics table below).

Review Biological Recovery Metrics

Threshold Recovery Metrics

The table below summarizes Recovery Metrics that have associated Recovery Thresholds. For each of these metrics, scenarios are evaluated to see what percentage or tributaries or years they achieve the recovery target for each scenario.

Value Performance measure Description Target/Recovery Threshold Percentage Reached in Kitchen Sink?
1: Salmonid abundance 1: Adult abundance Represents an interest in increasing salmonid abundance across the Central Valley. Can be estimated with models as annual number of adult spawning salmonids in each tributary and ocean, tracked for 20 years. Adult abundance for each year and tributary is a direct output from the SIT DSMs and is summarized to show average Central Valley annual abundance. 500 or more spawners for every Central Valley independent population in the last 10 years of the simulation. (every year, 8 out of 10 years) what is this?
2: Salmonid productivity 2.1: Cohort Replacement Represents an interest in having growing or stable salmonid populations. CRR can be estimated with models as the adult natural origin return ratio in each tributary, tracked for 20 years. CRR is calculated as the number of natural origin adult returns in year X+3 divided by the number of in-river spawners in year X. CRR is calculated for each year and tributary and then averaged across tributaries and years. Mean CRR > 1 for every Central Valley independent population in the last 10 years of the simulation.
2: Salmonid productivity 2.2: Population growth rate Represents an alternative way to capture growing or stable salmonid populations. Can be estimated with models as average trend in population growth over a 20-year period. Mean Growth Rate > 1 for every Central Valley independent population in the last 10 years of the simulation. (any leway here?)
4: Salmonid genetic diversity 4: pHOS Represents an interest in preserving genetic diversity of natural populations and minimizing potential negative demographic effects from hatchery origin fish. Salmonid models are currently being modified to estimate proportion of hatchery origin spawners (pHOS). pHOS < 5% for every Central Valley independent population in the last 10 years of the simulation. (every year, 8 out of 10 years) what is this?

Additional Biological Recovery Metrics

The table below provides additional recovery metrics to help balance and refine scenarios. This set of metrics does not have clear threshold values that indicate recovery but instead provides additional context to help select more balanced scenarios.

Value Performance measure Description TODO:How can we evaluate these for kitchen sink (a
3: Salmonid spatial structure 3.1: Independent populations Represents an interest in increasing and maintaining the distribution of salmonids across historically occupied watersheds. Watershed-specific abundance estimates from models can be used to calculate the number of independent viable populations in each diversity group per ESU/run.
3: Salmonid spatial structure 3.2: % of potential independent populations Represents an alternative way to capture the distribution of salmonid, calculated as the % of potential independent viable populations in each diversity group per ESU/run.
3: Salmonid spatial structure 3.3: Dependent populations Represents an interest in increasing and maintaining the distribution of salmonids across historically occupied watersheds. Watershed-specific CV Salmon Recovery abundance estimates from models can be used to calculate the number of dependent populations in each diversity group per ESU/run.
5: Salmonid life history diversity 5.1: Age distribution of spawning adults Represents an interest in preserving life history diversity (age of spawners) in natural populations. Salmonid models can be used to estimate the minimum % of each age class of adults and check if targets are met (Age 4 >35%, Age 5+ >20%).
5: Salmonid life history diversity 5.2: Size distribution of juveniles Represents an interest in preserving life history diversity (size distribution of juveniles) in natural populations. Salmonid models can be used to estimate the variation in juvenile abundance of each life stage (fry, parr, yearling) and calculate variation across years. Size distribution of juveniles is summarized in a single metric by using a Shannon diversity index.
5: Salmonid life history diversity 5.3: Size and timing of juveniles at ocean entry Represents an interest in preserving life history diversity (size and timing of juveniles at ocean entry) in natural populations. Size distribution and timing of juveniles at ocean entry is summarized in a single metric by using a Shannon diversity index.
5: Salmonid life history diversity 5.4: Habitat diversity

Represents an interest in preserving habitat diversity that facilitates life history diversity in natural populations. Could be estimated as the amount and relative % of available habitat of different types (measured in area and days). Specific methods using the salmon models to calculate and compare optimal habitat ratios to population growth are being developed.

TODO: update this to be floodplain over inchannel habitat (as starting point) - looking for evenness over the full rearing period (also present for wet years and dry year)
6: Abundance, productivity, and distribution at levels that support ecosystem health 6: Ecosystem health Represents an interest in maintaining resilient and functioning ecosystems due to adequate salmonid abundance. Could be captured with a proxy metric of ratio of spawner abundance to habitat (marine derived nutrient proxy). The marine derived nutrient proxy metric gives the grams of marine nutrient per square meters of river. To calculate marine derived nutrient proxy, we calculated the total acres by multiplying habitat extent lengths by river width. We then multiplied the average annual number of spawners by the average weight (assumed 21 grams) and divided by our total area CV Salmon Recovery Draft for Planning Team Review 11 (square meters) to get a grams of marine derived nutrient per square meters.
7: Biological recovery objectives met by certain time 7: Time to biological recovery Represents an interest to recover salmonids quickly. Can be estimated by salmon models as the # of years until recovery objectives are met. See Phase 1 report for a list of recovery objectives.

Review Kitchen Sink Scenario

The kitchen sink scenario includes efforts in each of the 4 knobs that we can turn in the R2R process: Habitat, Hydrology, Harvest (oceans & rivers) and Hatcheries. The table below summarizes the kitchen sink scenario in comparison to the Baseline scenario.

Recovery scenario Habitat Hydrology Harvest (oceans & rivers) Hatcheries
Baseline Current + planned Current operations Current levels Current operations
Kitchen sink

Max habitat

Food subsidies

Predation reduction

All years

Ecological Functional Flows (EFF)

All years

Harvest only hatchery fish (ocean/Commercial)

Intelligent CRR harvest* (in-river/Tribal, Recreational)

All years

Terminal hatchery/ocean outplanting (current release output number)

All years

Run Kitchen Sink Scenario

The following code block runs the kitchen sink scenario.

# Kitchen Sink --
new_params_ks <- fallRunDSM::r_to_r_kitchen_sink_params
new_params_ks$movement_hypo_weights <- c(1, rep(0, 7))

# BASELINE --
new_params <- fallRunDSM::r_to_r_baseline_params
new_params$movement_hypo_weights <- c(1, rep(0, 7))

# seed
r2r_seeds_ks <- fallRunDSM::fall_run_model(mode = "seed",
                                        ..params =  new_params, # seed with baseline, then kitchen sink
                                        delta_surv_inflation = TRUE)

# run model
r2r_model_results_ks <- fallRunDSM::fall_run_model(mode = "simulate",
                                                ..params =  new_params_ks,
                                                seeds = r2r_seeds_ks,
                                                delta_surv_inflation = TRUE)

Results

Model results should be evaluated relative to the Baseline model. The following plots show the % difference from baseline results for the Kitchen sink scenario. You can look at the tab to the right to see the total spawner trends of the Kitchen Sink Scenario in comparison to the Baseline Scenario. (Make add a percent difference table in here too) - Think through the best way to present these. Also add a percent difference bar plot)

% Difference from Baseline (all watersheds)

% Difference from Baseline (all watersheds)

Spawners Plot

Threshold Biological Performance Metrics

The two tabs below show plots that describe if a tributary meets the recovery objective.

Abundance and Genetic Diversity

Productivity Metrics

Additional Biological Performance Metics

Spatial Structure

Life History Diversity